I have been using Mendeley for my research paper library for some time and I absolutely love the way it takes care fo organizing my library. Is there such a Web/Desktop app to organize my ebook library. I would like to put all my PDFs (and other formats) in a giant folder and the app should take care of organizing them by author, publisher, isbn, tags etc

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Although NOT a web app, I use Calibre (http://calibre-ebook.com/) for my nook. It can manage eBooks and PDF docs. Additionally, it can download and convert RSS feeds. I use it like iTunes. It's open source and there is a version that runs on Windows, Apple and Linux.